[gmx-users] peptide goes out of box after md simulation

Bhawana Gupta bhawana.gupta2010 at gmail.com
Mon Nov 24 05:33:43 CET 2008

hello everyone,

After doing md simulation with no. of steps 1 ns ,my peptide which is of 7-8
residue move out of the boundary of water box.

tell me what shd i do get rid of this problem.
Also i want to know about the wall of the box, whether it is permeable or
this is very silly question.
Is there something, from which i can know about the dimension of the box and
about the membrane so that i can change it when i have to simulate a peptide

Thanks in advance
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